From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Fri Feb 09 2007 - 12:36:40 CST
Dear Mustapha,
as you should know, gromacs uses a united atom representation for
hydrogens, ie, hydrogen atoms are implicitly modeled. That's why you see
the difference in the number of atoms. Moreover, each forcefield has
it's own nomenclature for the atoms in the molecule, so you would have
to use aliases in psfgen in order to use that pdb. After that, the
missing hydrogens can be guessed.
I used to have a script to transform that exact file into charmm's
topology/coordinate files. As soon as I find it I will send it to you
(ok, IF i find it).
Regards
Cesar
mustapha.hamdi_at_ensi-bourges.fr escribió:
> Dear all,
>
> I'm trying to generate the DMPC membrane psf file using
> http://www.ucalgary.ca/~tieleman/files/dmpc_npat.pdb . I founded that the
> DMPC residue Charmm27 and Gromacs are not the same, the Gromacs DMPC
> residue have 46 atoms and Charmm top_all27_lipid one have 118 atoms. Is
> there a way to generate DMPC psf file ?
> PS: the attached: DMPC.pdb and DMPC gromacs topology file.
>
> Best regards,
>
>
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